MD Analysis Pre-Processed Data Input Files: Towards a New Model for the TREX1 Exonuclease, Hemphill et al.

All atoms molecular dynamics simulations were performed for TREX1 apoenzyme, TREX1-ssDNA complex, and TREX1-dsDNA complex, with four replicate simulations per system. Trajectory and initial condition output files were pre-processed in VMD to generate time-step sampled mol2 files of the macromolecules in each simulation. The mol2 files were used to calculate phi/psi angles of the protein backbone, and to extract all-atoms coordinate information over time, and this information was organized into an RData file for each simulation system, including all simulation replicates. These RData files are provided, and they were analyzed with the scripts described in the affiliated manuscript.